College of Computer, Mathematical & Natural Sciences

Permanent URI for this communityhttp://hdl.handle.net/1903/12

Effective October 4, 2010, the University established the College of Computer, Mathematical, and Natural Sciences (CMNS) by integrating the former colleges of Chemical and Life Sciences (CLFS) and Computer Mathematical and Physical Sciences (CMPS).

The collections in this community comprise faculty research works, as well as graduate theses and dissertations.

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Now showing 1 - 10 of 6772
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    A Facile Synthesis of Bulk LiPON in Solution for Solid-State Electrolyte
    (2025) Gomez, Osma; Antar, Adam; Hall, Alex; Tapia-Aracayo, Leopoldo; Seo, Joshua; Kim, Nam; Sun, Zihan; Lim, Ryan; Chen, Fu; Li, Yue; Cumings, John; Rubloff, Gary; Lee, Sang Bok; Stewart, David; Wang, Yang; Lee, Sang Bok; Cumings, John; Rubloff, Gary
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    Lava River Cave IMU (Moasure) Traverse
    (2025) Wang, Jingchuan; Schmerr, Nicholas; Porter, Ryan; Whelley, Patrick
    Lava River Cave near Flagstaff, Northern Arizona, is a lava tube approximately 1.25 km long and 15 m wide. The cave has been previously mapped by manual sketching and, recently, mobile light detection and ranging (LiDAR; King et al., 2023). However, large discrepancies remain in the absolute positioning of the cave passage, likely owing to poor GPS reception in the pine forest. To address this inconsistency, we performed a 350 m traverse of the cave passage starting at the cave entrance and ending at the pillar where the tube bifurcates and reconnects, while tracking the movement using a Moasure 2 PRO, a motion-based measuring tool (inertial measurement unit). The resulting 3D spatial dataset in Cartesian coordinates was then georeferenced using a straight path north of the cave and the nearby parking lot as base stations.
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    Insoluble Acyclic Cucurbit[n]uril-Type Receptors Capture Iodine from the Vapor Phase
    (Wiley: Chemistry European Journal, 2024-09-27) Perera, Suvenika; Shaurya, Alok; Zeppuhar, Andrea; Chen, Fu; Zavalij, Peter Y.; Gaskell, Karen; Isaacs, Lyle; Isaacs, Lyle
    Nuclear energy makes large contributions toward meeting global energy needs, but societal concerns remain high given the impacts of the intended release of radioactive materials including 129I and 131I. In this paper we explore the use of a homologous series of acyclic CB[n] type hosts (H1–H4) as adsorbents of iodine from the vapor phase. We find that H2–H4, but not H1 – perform well in this application with uptake capacities of 2.2 g g−1, 1.5 g g−1, and 1.9 g g−1, respectively. The chemisorptive uptake process involves partial oxidation of catechol walled H2 to quinone walled host and capture of I3− and I5−. Solid H2 can be regenerated by treatment with Na2S2O4 and reused at least five times. The x-ray crystal structure of H2 is also reported.
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    A Swarm of WASP Planets: Nine giant planets identified by the WASP survey
    (2025) Schanche, Nicole
    The Wide Angle Search for Planets (WASP) survey provided some of the first transiting hot Jupiter candidates. With the addition of the Transiting Exoplanet Survey Satellite (TESS), many WASP planet candidates have now been revisited and given updated transit parameters. In the accompanying paper, we present 9 transiting planets orbiting FGK stars that were identified as candidates by the WASP survey and measured to have planetary masses by radial velocity measurements. Subsequent space-based photometry taken by TESS as well as ground-based photometric and spectroscopic measurements have been used to jointly analyze the planetary properties of WASP-102 b, WASP-116 b, WASP-149 b WASP-154 b, WASP-155 b, WASP-188 b, WASP-194 b/HAT-P-71 b, WASP-195 b, and WASP-197 b. These planets have radii between 0.9 R_Jup and 1.4 R_Jup, masses between 0.1 M_Jup and 1.5 M_Jup, and periods between 1.3 and 6.6 days.
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    Active Seismic Exploration of Planetary Subsurfaces via Compressive Sensing
    (2025) Wang, Jingchuan; Schmerr, Nicholas; Lekic, Vedran
    The software supports the following study: We present a method for improving seismic data collection on planetary surfaces such as the Moon and Mars. This approach is based on recent advances in compressive sensing technology to reduce the number of data collection points required compared to conventional methods without sacrificing the quality of the resulting subsurface images. We demonstrate its effectiveness using both synthetic and field data from locations with similarities to planetary surface environments. The method is then applied to reanalyze seismic data collected by the crew of the Apollo 14 and 16 missions. Our study has implications for mission planning, as this method can make space missions more efficient by reducing the equipment and time to collect geophysical data on planetary surfaces. It also makes it possible to reconstruct missing or damaged data, improving the quality of imagery and enhancing our understanding of the interior of other worlds.
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    TREE GENETICS AND GREENSPACE MANAGEMENT INTENSITY INFLUENCE URBAN TREE INSECT COMMUNITIES, DAMAGE, AND FOLIAR TRAITS
    (2024) Perry, Eva Emma; Burghardt, Karin T; Entomology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Trees are essential to well-functioning urban systems, providing services that benefit humans and wildlife. For example, arthropods that use trees in cities perform key roles in the urban food web as both prey and predators, but they can also be vulnerable to environmental stressors associated with cities. Previous work documents broad patterns in arthropod communities associated with management practice gradients in urban areas. How these patterns relate to changes in tree genetic background across management types remains a largely unexplored topic. To disentangle the genetic and management associated effects on arboreal insect abundance, communities, and foliar damage, I repeatedly sampled trees of known genetic relatedness for two commonly planted tree species: Acer rubrum (n = 65), and its non-native congener Acer platanoides (n = 71), in June and August of 2023 and 2024. I systematically selected about 3 individual trees growing in four human management intensity categories (street trees, parks and residential yards, urban forest patches, or rural forests) for each of 5 genetic lineages per tree species. I used vacuum sampling to collect mobile arthropods from the lower canopy of each focal tree in June and August of 2023 and 2024, and identified samples to order. I also assessed insect and systemic foliar damage, gall abundance, and select physiological traits in August 2024. I found the general trend of increasing total arthropod abundance with increasing management intensity. However, management effects differed across genetic background with almost ubiquitous interactions between management type and genetic lineage. The most dominant group of insects found on study trees belonged to the order Hemiptera. This group of primarily herbivorous piercing/sucking insects were the primary drivers of these overarching abundance patterns. Spiders, which were the most abundant primarily predatory arthropod order, exhibited the opposite pattern, increasing in overall abundance in the later season, decreasing with increasing management intensity, and generally not responding to tree genetic lineage. In 2024, increasing management intensity negatively affected cumulative insect herbivore damage and gall abundance, and did not vary by genetic lineage. Gall formers were found only on native Acer rubrum, with no galls sampled from the non-native A. platanoides. In contrast, systemic foliar damage did not change with management, and only varied by tree genetic lineage for Acer platanoides. Foliar photosynthetic traits’ variance by management intensity or tree genetic lineage was species dependent; A. rubrum traits varied by tree genetic lineage, while A. platanoides traits varied by management intensity. Overall, my results suggest that tree genetic background plays an important role in mediating management effects on insect populations, particularly for piercing-sucking herbivorous species, but genetic background’s effect on other metrics such as foliar damage and traits may be species-specific. Further studies should be sure to consider the structure of genetic populations when describing patterns of insect use. Results of this thesis will serve to inform best practices for urban tree management and pest mitigation, as cities work to maintain and increase urban canopy cover.
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    SENSORY AND HORMONAL MECHANISMS OF EARLY LIFE BEHAVIOR IN A SOCIAL CICHLID FISH
    (2024) Westbrook, Molly; Juntti, Scott; Biology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Studying the ontogeny of animal behavior is fundamental to ethology and allows understanding how behaviors in early life may affect later life success. The social cichlid Astatotilapia burtoni is an excellent model for examining the mechanisms of early life aggression due to the robust social hierarchy enforced by stereotyped, measurable social behaviors. We examine how hormonal signaling affects early life aggression through pharmacology and CRISPR-Cas9 mutants. We test which sensory pathways convey aggression-eliciting stimuli through sensory deprivation experiments. And we identify kinematic features that predict aggression through machine-learning video tracking algorithms. We observe that aggressive behaviors emerge around 17 days post fertilization (dpf), correlating with when the animals transition to free swimming away from the mother. We find that sex steroids subtly organize behavioral circuits for aggression and suggest that unknown additional mechanisms play a leading role. We show that thyroid hormone is not necessary or sufficient for the transition to aggressive behavior. We show that visual signals are necessary for the full expression of aggression, but in the absence of visual signal, low levels of aggression remain. We show that ciliated olfactory receptor signaling maintains low levels of aggression, as mutant animals display higher levels of aggressive behavior between 17 and 24 dpf. Finally, we demonstrate that swimming velocity has potential to predict aggressive instances of behavior. Together, we find multiple levels of control for early life aggressive bouts from sensory input to hormonal organization of brain circuits.
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    GEOMORPHIC AND HYDROLOGIC CHARACTERISTICS OF SMALL URBANIZED TRIBUTARIES TO A FALL ZONE STREAM
    (2024) Harris, John Allen; Prestegaard, Karen; Geology; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Many rivers along the Atlantic Coast contain major knickpoints, which define the Fall Zone. These often-urbanized rivers straddle multiple physiographic regions with spatial variations in lithology, topography, and hydrology. This research evaluates the effects of mainstem channel incision and urbanization on channel and catchment morphology, bed substrate mobility, catchment water storage dynamics, and hydrologic response in tributaries of the Northwest Branch of the Anacostia River above and below the Fall Zone knickpoint. Topographic analyses show that differential incision below the mainstem knickpoint has initiated steep secondary channels incised into bedrock. Measurements at representative reaches show that bankfull shear stress exceeds critical shear stress in these newly initiated tributaries, resulting in erosive channels outside of threshold conditions. Increased urban runoff introduced at storm drain outfalls maintains these non-steady state conditions. Geophysical surveys reveal that regolith depth for water storage capacity is primarily below the flatter ridgetops of the tributary catchments, where development is concentrated. The secondary tributaries cannot access these upland storage zones, and thus have limited infiltration and recharge capacity. I installed streamgages in the tributaries and constructed catchment water balances to study storage dynamics and hydrologic response. Hydrologic consequences of urbanizing the steep secondary tributaries include flashy, elevated stormflows, greater total runoff, and reduced baseflows that are not maintained during drought periods. The combination of steep channels, thin regolith, and urban overprint limits infiltration to moderate storm responses and recharge storage. These effects were not seen in non-urbanized secondary tributaries, urbanized tributaries above the knickpoint, or the forested reference streams above the Fall Zone. These findings define the geomorphic adjustment of tributaries to differential mainstem incision and explore the hydrologic impacts of urbanizing small steep catchments with limited effective storage capacity. Supplementary files:S1: Table with the location, drainage area, stream gradient, bankfull hydraulic values, and grain size values at each Northwest Branch tributary and reference reach used in the study. S2: Spreadsheet with the water level logger gage height values collected at 5-minute intervals from April 2023-March 2024 and calculated discharge from the Northwest Branch tributary streamgages. S3: Spreadsheet with the monthly water balance values for the Northwest Branch tributary catchments and reference watersheds from April 2023-March 2024. S4: Table with the depth to bedrock values and corresponding slope angles measured from the seismic profiles and LiDAR-derived digital elevation models.
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    THE ROLE OF GENOME ORGANIZATION AND FILAMENTOUS BACTERIOPHAGE ON GONOCOCCAL BIOLOGY AND PATHOGENICITY
    (2024) Kopew, Jessica; Stein, Daniel C; Cell Biology & Molecular Genetics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Gonorrhea, caused by the bacterium Neisseria gonorrhoeae (GC), represents a significant global health concern as it is the second most common bacterial STI and has a rising rate of antimicrobial resistance. The first study of this thesis aims to elucidate the causes and consequences of gonococcal genome reorganization. Here I found that when looking at many GC strains’ genomes, each GC strain had a unique genome organization including both inversions and translocation events. I also saw a consistent pattern of DNA high sequence similarity on both sides of the translocation or inversions, consistent with homologous recombination driven reorganization. PCR analysis of inversion events suggests that these large-scale reorganization events are both stable and rare. Growth curve analysis demonstrates a wide variability in growth rate between strains. Proteomic analysis suggests reorganization driven changes to replication termination location leads to upregulation of many kinds of proteins including energy metabolism and antimicrobial resistance associated genes. This study suggests that homologous recombination driven genome reorganization can have large impacts on gonococcal biology and pathogenicity. This study demonstrates the need for future gonococcal studies to use multiple GC strains from a diverse background to capture the wide variability in GC phenotypes. The second study of this thesis sought to uncover the role filamentous bacteriophage play in GC biology. I found that every GC strain currently in the NCBI database at the date of this study contains four filamentous bacteriophage gene regions in the GC genome. I found that FA1090Δfil (a GC strain lacking all four filamentous bacteriophage gene regions) grew poorly at 37⁰C both in broth and on agar, as compared to wild type FA1090. However, there was no difference when the strains were grown at 34⁰C or when grown without shaking, demonstrating the condition dependent nature of this growth advantage. FA1090Δfil formed larger bacterial aggregates than FA1090 WT. When these strains were analyzed for their ability to produce biofilms, no differences were seen in the overall biofilm’s biomass, yet the overall structure of the biofilms were different, with FA1090Δfil producing taller and rougher biofilms. Previous unpublished research in the Stein Lab demonstrates that filamentous phage derived proteins are capable of deteriorating the integrity of epithelial cell cultures and cervical tissue explants. The data from this chapter suggests that filamentous phage provide the gonococcus with a growth advantage, inhibit bacterial aggregation, alter the structure of the GC biofilm, and that phage proteins can lead to loss of the integrity of the epithelium. Taken en toto, these studies demonstrate that both alterations in bacterial genome organization and contributions from filamentous bacteriophage genomes can impact gonococcal biology and pathogenicity, which could be key to preventing and treating GC infections.
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    INITIAL LOCAL CYTOKINE RESPONSES AGAINST NEISSERIA GONORRHOEAE INFECTIONS IN THE HUMAN CERVIX
    (2024) Dai, Yiwei; Song, Wenxia; Cell Biology & Molecular Genetics; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Neisseria gonorrhoeae (GC) is a human-specific pathogen that causes gonorrhea, a common sexually transmitted infection. In women, GC initiate infection by colonizing the cervix. Although GC colonization can cause cervicitis, most female infections are asymptomatic. Asymptomatic colonization of the cervix increases the risk of transmission and progression to severe complications, including pelvic inflammatory disease and infertility. Despite its clinical significance, the mechanisms underlying GC asymptomatic colonization remain unclear. Using a human cervical tissue explant model, which can mimic GC infection in vivo, my Ph.D. research examined the early local cytokine responses to GC cervical colonization, a determining factor for asymptomatic and symptomatic clinical outcomes. Luminex and spatial transcriptomic analyses found that cervical tissue explants constitutively secrete and express a broad spectrum of cytokines, with particularly high levels of the IL-1 receptor antagonist IL-1RA, the anti-inflammatory cytokines IL-10, and the multi-functional cytokine IL-6. During the first 24-h inoculation, GC strain expressing an opacity-associated protein binding to the host receptor CEACAMs (MS11OpaCEA) increased the secretion and transcript levels of both pro-inflammatory, like IL-1α/β, and the anti-inflammatory cytokine IL-10, as well as multi-functional cytokines, like IL-6 and CFS3, but MS11 lacking Opa (MS11∆Opa) induced much less. Notable, the cervix secreted IL-1RA at 100-fold higher levels than IL-1α/β. Cervical secreting levels of soluble IL-6 receptors, required for activating IL-6 inflammatory functions, were 10,000-fold less than IL-6. These results support an anti-inflammatory-dominated cytokine environment of the human cervix, and GC further push it in the anti-inflammatory direction. Using isogenic GC strains and inhibitors, the mechanism underlying GC cytokine induction and the impact of GC-induced cytokines on GC infection were examined. My research found that GC-induced inflammatory cytokine production involved NF-κB activation in both epithelial and subepithelial cells. GC-induced IL-10 production depended on the activation of CEACAM-downstream signaling molecule SHP1/2. Reductions in inflammatory cytokines, TNF-α and IL-1β, by an NF-κB inhibitor did not significantly affect GC colonization, epithelial cell-cell junctions, or epithelial shedding. In contrast, neutralizing IL-10 or blocking its receptor reduced GC colonization and increased ectocervical epithelial shedding and disassembly of epithelial cell-cell junctions. Thesis results suggest that IL-10 plays critical roles in strengthening the cervical epithelium and suppressing the epithelial cell-cell junction disrupting function of inflammatory cytokines, and that GC further elevate the local IL-10 level to prevent bacteria from shedding off with epithelial cells, enhancing colonization.Immunofluorescence and spatial transcriptomic approaches were utilized to identify the types of cervical cells contributing to the local cytokine response to GC infection. Cervical epithelial cells and macrophages are two of the major contributors. IL-1RA protein and mRNA were primarily detected at the ectocervical epithelium. IL-6 protein and mRNA were also detected in ectocervical epithelial cells. MS11OpaCEA colonization increased IL-1RA transcript levels, while MS11ΔOpa switched ectocervical epithelial cells from IL-1RA- to IL-8/IL-6-expressing. GC inoculation did not alter the transcriptomic program of CD68+ macrophages adjacent to the ectocervical epithelium, maintaining the tissue-repair signature. However, GC changed the transcriptomic profiles of macrophages at the explant tissue side, exposed to media and inoculated GC, leading to increased expression of either inflammatory M1- or anti-inflammatory M2 signature genes. These results suggest that the human cervix utilizes high levels of epithelial-secreted IL-RA, low levels of soluble IL-6 receptor release, and tissue-repairing macrophages at the subepithelium to control inflammation induced by colonizing GC when the epithelium prevents GC from entering the tissue. Overall, my research results suggest that GC exploit the local cytokine response of the human cervix, dominant by anti-inflammatory IL-1RA, IL-10, and IL-6, to facilitate colonization and desensitize immune detection, promoting asymptomatic colonization.